2M58
Structure of 2'-5' AG1 lariat forming ribozyme in its inactive state
Summary for 2M58
| Entry DOI | 10.2210/pdb2m58/pdb |
| NMR Information | BMRB: 19040 |
| Descriptor | RNA (59-MER) (1 entity in total) |
| Functional Keywords | rna, lariat, 2'-5' branching |
| Biological source | synthetic |
| Total number of polymer chains | 1 |
| Total formula weight | 19163.36 |
| Authors | Carlomagno, T.,Amata, I.,Codutti, L.,Falb, M.,Fohrer, J.,Simon, B. (deposition date: 2013-02-18, release date: 2013-04-03, Last modification date: 2024-05-15) |
| Primary citation | Carlomagno, T.,Amata, I.,Codutti, L.,Falb, M.,Fohrer, J.,Masiewicz, P.,Simon, B. Structural principles of RNA catalysis in a 2'-5' lariat-forming ribozyme. J.Am.Chem.Soc., 135:4403-4411, 2013 Cited by PubMed Abstract: RNA-catalyzed lariat formation is present in both eukaryotes and prokaryotes. To date we lack structural insights into the catalytic mechanism of lariat-forming ribozymes. Here, we study an artificial 2'-5' AG1 lariat-forming ribozyme that shares the sequence specificity of lariat formation with the pre-mRNA splicing reaction. Using NMR, we solve the structure of the inactive state of the ribozyme in the absence of magnesium. The reaction center 5'-guanosine appears to be part of a helix with an exceptionally widened major groove, while the lariat-forming A48 is looped out at the apex of a pseudoknot. The model of the active state built by mutational analysis, molecular modeling, and small-angle X-ray scattering suggests that A48 is recognized by a conserved adenosine, juxtaposed to the 5'-guanosine in one base-pair step distance, while the G1-N7 coordinates a magnesium ion essential for the activation of the nucleophile. Our findings offer implications for lariat formation in RNA enzymes including the mechanism of the recognition of the branch-site adenosine. PubMed: 23472843DOI: 10.1021/ja311868t PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
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